Hebner debuted in the World Wrestling Federation as a referee during a WWF Championship match pitting champion Hulk Hogan against challenger André the Giant, which aired live on February 5, 1988, on NBC's The Main Event. In the storyline, Hebner's twin brother Dave Hebner was the assigned official, but unbeknownst to Hogan, André's manager Ted DiBiase had bribed an unknown to get plastic surgery to look like Hebner (Earl and Dave are identical twins, so this was easy to pull off). Earl then counted André's pin against Hogan, even though Hogan's shoulders were clearly off the mat. As André and DiBiase were celebrating (with André quickly "selling" his title to an overjoyed DiBiase), Dave (whom DiBiase had locked in a closet prior to the match) ran to the ring and confronted Earl. The two brothers argued, and then they fought each other in the middle of the ring. Hulk Hogan, figuring out that Dave's "evil twin" had jobbed him out, picked Earl up and gorilla press slammed him over the ropes and onto the aisleway (missing DiBiase).

This match helped set up a 14-man elimination tournament at WrestleMania IV, since WWF President Jack Tunney declared the title "vacant" a week after The Main Event match as the WWF Championship "cannot be bought or sold," where the winner would win the WWF Championship. Vince McMahon paid both Hebners a bonus of $2,500 for participating in the angle.

Meanwhile, the WWF continued to build heat for Earl Hebner through a kayfabe "investigative report" published in the promotions' flagship publication, WWF Magazine.

The most infamous event in Hebner's career—and possibly in the history of professional wrestling in North America—came during the main event of the 1997 Survivor Series in what has since been dubbed the "Montreal Screwjob." During a match for the WWF Championship between then-champion Bret Hart and challenger Shawn Michaels, Hebner signaled for the timekeeper to ring the bell (signifying the end of the match) while Michaels had Hart in a Sharpshooter hold—Hart's long-established signature move—even though Hart visibly had not submitted. Michaels had thus "won" the WWF Championship. This was not the match ending that Hart had asked for. Hebner had, at the behest of Vince McMahon, "screwed" Hart out of the title. He therefore decided to forcibly remove the title from Hart by instructing Hebner (who had previously promised Hart "on his children's lives" that he would not betray him) to signal an end to the bout when Michaels had Hart in a submission hold. The fallout of the screwjob led to a large degree of antagonism towards Hebner, McMahon, and Michaels, especially in Canada, where fans often chant "You screwed Bret!" at the offending parties.

Hebner was involved in several storylines. He spearheaded the (kayfabe) referee's strike in 1999, resulting in referees being given the authority to defend themselves if physically provoked by wrestlers. In early 2000, he cost Triple H his WWF Championship by quick-counting during a match between Triple H and Chris Jericho following weeks of abuse by Triple H. Triple H eventually forced Hebner to reverse the decision, promising never to lay his hands on Hebner as long as Hebner was a WWF employee. After Hebner took the title from Jericho and gave it back to Triple H, Triple H "fired" Hebner and promptly Pedigreed him and beat him unconscious. Hebner was reinstated by Linda McMahon thirteen days later, replacing corrupt guest referee Shane McMahon during a title match between Triple H and The Rock at Backlash 2000 and counting the fall when The Rock covered Triple H for the pin. During the Invasion angle in late 2001, Hebner became involved in a feud involving referee Nick Patrick. Patrick was a biased referee who often helped The Alliance achieve victories over their WWF opponents. Hebner defeated Patrick in a match at WWF Invasion.

Hebner was released from WWE on July 18, 2005.

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